Starting phenix.real_space_refine on Tue Feb 13 09:33:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz1_15031/02_2024/7zz1_15031.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Mg 1 5.21 5 S 24 5.16 5 C 3110 2.51 5 N 829 2.21 5 O 993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 498": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 952": "OD1" <-> "OD2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1081": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B GLU 1135": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4958 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4301 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 576 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 1, ' MN': 1, 'OAA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Time building chain proxies: 3.47, per 1000 atoms: 0.70 Number of scatterers: 4958 At special positions: 0 Unit cell: (69.96, 76.32, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 24 16.00 Mg 1 11.99 O 993 8.00 N 829 7.00 C 3110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 925.3 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 4 sheets defined 54.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.512A pdb=" N MET A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.873A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.640A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.503A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.648A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.934A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.527A pdb=" N LYS A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 861 Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 886 through 894 removed outlier: 3.517A pdb=" N TYR A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 945 through 958 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.764A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 733 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1070 through 1072 removed outlier: 8.202A pdb=" N LEU B1133 " --> pdb=" O LEU B1119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU B1119 " --> pdb=" O LEU B1133 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU B1135 " --> pdb=" O VAL B1117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B1117 " --> pdb=" O GLU B1135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1077 through 1078 Processing sheet with id=AA4, first strand: chain 'B' and resid 1097 through 1100 removed outlier: 4.174A pdb=" N MET B1097 " --> pdb=" O ILE B1108 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1630 1.34 - 1.46: 1030 1.46 - 1.58: 2293 1.58 - 1.70: 1 1.70 - 1.82: 46 Bond restraints: 5000 Sorted by residual: bond pdb=" C3 BTN B1201 " pdb=" O3 BTN B1201 " ideal model delta sigma weight residual 1.220 1.409 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C2 BTN B1201 " pdb=" S1 BTN B1201 " ideal model delta sigma weight residual 1.824 1.671 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 1.329 1.427 -0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" C3 OAA A1203 " pdb=" O3 OAA A1203 " ideal model delta sigma weight residual 1.214 1.306 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 4995 not shown) Histogram of bond angle deviations from ideal: 91.17 - 99.76: 1 99.76 - 108.34: 230 108.34 - 116.92: 3235 116.92 - 125.51: 3230 125.51 - 134.09: 68 Bond angle restraints: 6764 Sorted by residual: angle pdb=" CA GLN B1130 " pdb=" CB GLN B1130 " pdb=" CG GLN B1130 " ideal model delta sigma weight residual 114.10 125.45 -11.35 2.00e+00 2.50e-01 3.22e+01 angle pdb=" CA LYS B1062 " pdb=" CB LYS B1062 " pdb=" CG LYS B1062 " ideal model delta sigma weight residual 114.10 124.11 -10.01 2.00e+00 2.50e-01 2.50e+01 angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 115.88 7.12 1.60e+00 3.91e-01 1.98e+01 angle pdb=" CA GLU B1064 " pdb=" CB GLU B1064 " pdb=" CG GLU B1064 " ideal model delta sigma weight residual 114.10 122.37 -8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CB GLN B1094 " pdb=" CG GLN B1094 " pdb=" CD GLN B1094 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.70e+00 3.46e-01 1.43e+01 ... (remaining 6759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.67: 2842 29.67 - 59.34: 170 59.34 - 89.00: 19 89.00 - 118.67: 0 118.67 - 148.34: 1 Dihedral angle restraints: 3032 sinusoidal: 1247 harmonic: 1785 Sorted by residual: dihedral pdb=" C1 OAA A1203 " pdb=" C2 OAA A1203 " pdb=" C3 OAA A1203 " pdb=" O3 OAA A1203 " ideal model delta sinusoidal sigma weight residual -102.23 46.11 -148.34 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA LYS B1123 " pdb=" C LYS B1123 " pdb=" N GLY B1124 " pdb=" CA GLY B1124 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA THR A 886 " pdb=" C THR A 886 " pdb=" N GLU A 887 " pdb=" CA GLU A 887 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 538 0.046 - 0.092: 163 0.092 - 0.139: 39 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 749 Sorted by residual: chirality pdb=" CB ILE A 813 " pdb=" CA ILE A 813 " pdb=" CG1 ILE A 813 " pdb=" CG2 ILE A 813 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2 BTN B1201 " pdb=" C4 BTN B1201 " pdb=" C7 BTN B1201 " pdb=" S1 BTN B1201 " both_signs ideal model delta sigma weight residual False 3.08 2.87 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL B1084 " pdb=" CA VAL B1084 " pdb=" CG1 VAL B1084 " pdb=" CG2 VAL B1084 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 746 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.032 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C VAL A 702 " -0.101 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.038 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B1130 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLN B1130 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN B1130 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B1131 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1098 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL B1098 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B1098 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B1099 " -0.012 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 223 2.71 - 3.26: 4973 3.26 - 3.80: 9171 3.80 - 4.35: 11387 4.35 - 4.90: 18305 Nonbonded interactions: 44059 Sorted by model distance: nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.159 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1330 " model vdw 2.162 2.320 nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.195 2.320 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.216 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.235 2.400 ... (remaining 44054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.520 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 5000 Z= 0.429 Angle : 0.895 12.264 6764 Z= 0.474 Chirality : 0.048 0.231 749 Planarity : 0.006 0.062 883 Dihedral : 18.254 148.341 1888 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.68 % Allowed : 21.65 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.31), residues: 611 helix: -0.74 (0.26), residues: 285 sheet: -0.04 (0.74), residues: 43 loop : -0.59 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 799 HIS 0.010 0.001 HIS A 823 PHE 0.013 0.002 PHE A 907 TYR 0.015 0.002 TYR A 853 ARG 0.014 0.001 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.560 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 1.2286 time to fit residues: 85.9261 Evaluate side-chains 63 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 882 GLN B1128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5000 Z= 0.216 Angle : 0.544 5.977 6764 Z= 0.288 Chirality : 0.041 0.146 749 Planarity : 0.004 0.037 883 Dihedral : 9.012 142.825 715 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.64 % Allowed : 19.73 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.33), residues: 611 helix: 0.93 (0.29), residues: 289 sheet: -0.08 (0.74), residues: 43 loop : -0.39 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.011 0.001 PHE A 907 TYR 0.012 0.001 TYR A 853 ARG 0.007 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.530 Fit side-chains REVERT: A 569 TRP cc_start: 0.9627 (OUTLIER) cc_final: 0.8920 (t60) REVERT: B 1123 LYS cc_start: 0.8811 (mppt) cc_final: 0.8580 (mppt) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 1.2723 time to fit residues: 82.2238 Evaluate side-chains 60 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5000 Z= 0.181 Angle : 0.531 9.719 6764 Z= 0.276 Chirality : 0.041 0.151 749 Planarity : 0.003 0.033 883 Dihedral : 8.445 141.054 701 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.45 % Allowed : 19.16 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.34), residues: 611 helix: 1.46 (0.30), residues: 290 sheet: -0.10 (0.75), residues: 43 loop : -0.36 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.009 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.005 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.619 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8826 (mppt) cc_final: 0.8623 (mppt) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 1.2913 time to fit residues: 83.5602 Evaluate side-chains 59 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5000 Z= 0.369 Angle : 0.596 7.146 6764 Z= 0.315 Chirality : 0.044 0.156 749 Planarity : 0.004 0.036 883 Dihedral : 8.877 142.425 701 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.41 % Allowed : 18.58 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.34), residues: 611 helix: 1.58 (0.31), residues: 290 sheet: -0.22 (0.73), residues: 43 loop : -0.33 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 569 HIS 0.007 0.001 HIS A 823 PHE 0.009 0.001 PHE A 907 TYR 0.016 0.002 TYR A 853 ARG 0.004 0.001 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.606 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 67 average time/residue: 1.3421 time to fit residues: 93.7205 Evaluate side-chains 60 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5000 Z= 0.208 Angle : 0.543 6.246 6764 Z= 0.285 Chirality : 0.041 0.151 749 Planarity : 0.003 0.032 883 Dihedral : 8.557 142.012 701 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.64 % Allowed : 19.54 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.35), residues: 611 helix: 1.66 (0.31), residues: 291 sheet: -0.36 (0.73), residues: 43 loop : -0.26 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.010 0.001 PHE A 879 TYR 0.013 0.001 TYR A 853 ARG 0.004 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.607 Fit side-chains REVERT: A 705 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9142 (pmm) REVERT: B 1118 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7264 (p0) outliers start: 19 outliers final: 11 residues processed: 66 average time/residue: 1.2980 time to fit residues: 89.2793 Evaluate side-chains 64 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5000 Z= 0.180 Angle : 0.550 9.968 6764 Z= 0.283 Chirality : 0.041 0.149 749 Planarity : 0.003 0.031 883 Dihedral : 8.370 140.909 701 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.45 % Allowed : 20.88 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 611 helix: 1.75 (0.31), residues: 291 sheet: -0.37 (0.73), residues: 43 loop : -0.25 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.010 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.609 Fit side-chains REVERT: B 1088 ASP cc_start: 0.3586 (OUTLIER) cc_final: 0.3115 (OUTLIER) outliers start: 18 outliers final: 11 residues processed: 64 average time/residue: 1.3175 time to fit residues: 87.9731 Evaluate side-chains 61 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5000 Z= 0.233 Angle : 0.574 9.270 6764 Z= 0.299 Chirality : 0.043 0.282 749 Planarity : 0.003 0.032 883 Dihedral : 8.504 141.022 701 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 21.07 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 611 helix: 1.72 (0.31), residues: 291 sheet: -0.42 (0.72), residues: 43 loop : -0.26 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.025 0.002 PHE A 846 TYR 0.013 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.574 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 1.2998 time to fit residues: 85.4044 Evaluate side-chains 59 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5000 Z= 0.207 Angle : 0.556 7.922 6764 Z= 0.289 Chirality : 0.041 0.149 749 Planarity : 0.003 0.031 883 Dihedral : 8.379 140.552 701 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.83 % Allowed : 20.69 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 611 helix: 1.74 (0.31), residues: 291 sheet: -0.44 (0.73), residues: 43 loop : -0.29 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.014 0.001 PHE A 846 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.621 Fit side-chains REVERT: A 813 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (tp) outliers start: 20 outliers final: 13 residues processed: 65 average time/residue: 1.2562 time to fit residues: 85.2551 Evaluate side-chains 62 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 60 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5000 Z= 0.176 Angle : 0.568 8.190 6764 Z= 0.293 Chirality : 0.041 0.148 749 Planarity : 0.003 0.030 883 Dihedral : 8.258 139.842 701 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.87 % Allowed : 21.65 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 611 helix: 1.77 (0.31), residues: 291 sheet: -0.42 (0.74), residues: 43 loop : -0.26 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.012 0.001 PHE A 846 TYR 0.011 0.001 TYR A 853 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.591 Fit side-chains REVERT: A 813 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7912 (tp) REVERT: B 1123 LYS cc_start: 0.8824 (mppt) cc_final: 0.8605 (mppt) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 1.2603 time to fit residues: 82.8921 Evaluate side-chains 60 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN B1128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5000 Z= 0.209 Angle : 0.568 10.008 6764 Z= 0.293 Chirality : 0.042 0.149 749 Planarity : 0.003 0.031 883 Dihedral : 8.304 139.884 699 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 21.26 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.35), residues: 611 helix: 1.74 (0.31), residues: 291 sheet: -0.41 (0.74), residues: 43 loop : -0.26 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.015 0.001 PHE A 846 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.572 Fit side-chains REVERT: A 813 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7939 (tp) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 1.2750 time to fit residues: 78.5547 Evaluate side-chains 59 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054919 restraints weight = 14266.606| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.91 r_work: 0.3037 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5000 Z= 0.208 Angle : 0.593 10.361 6764 Z= 0.304 Chirality : 0.041 0.148 749 Planarity : 0.003 0.031 883 Dihedral : 8.267 139.659 699 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 21.84 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.35), residues: 611 helix: 1.74 (0.31), residues: 291 sheet: -0.43 (0.74), residues: 43 loop : -0.25 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 823 PHE 0.014 0.001 PHE A 846 TYR 0.011 0.001 TYR A 853 ARG 0.003 0.000 ARG B1061 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.36 seconds wall clock time: 41 minutes 25.65 seconds (2485.65 seconds total)